[gmx-users] Step size too small
omovie_johnnie at hotmail.com
Tue Aug 21 17:26:38 CEST 2007
Both Tom's and Mark's suggestions will fix the problem. The reason it did not work before now in my case, was that the molecules were almost overlying (almost same coordinates in structure file), thus the inf values I got.
I created some distance between them along one axis and was able to move on with EM and simulation.
> From: erikm at xray.bmc.uu.se> Subject: Re: [gmx-users] Step size too small> Date: Mon, 20 Aug 2007 10:07:09 +0200> To: gmx-users at gromacs.org> > > 17 aug 2007 kl. 21.46 skrev TJ Piggot:> > > Hi,> >> > I do not think that what Per suggests is the problem, if you look > > at the potential energy after the minimisation this value is huge > > (and the other two values are inf!). The problem is most likely > > with your topology. As you say the two molecules have been > > successfully minimised on their own so I would suggest that your > > problem is with either how you edit the .top file or the distance > > restraint between the molecules. For my protein that has more than > > one identical chains pdb2gmx does not recognise them as one if you > > provide different chain identifiers in the pdb file, so doing this > > should hopefully stop you having to edit the .top file.> >> > Yes. Just removing bonds in the top-file is not a good solution. > Breaking bonds changes the electronic structure of the molecule, > which in turn is represented by different atom types, so you would > need to change them as well, depending on the force field. Have you > tried the -nomerge option for pdb2gmx?> > /Erik> > > Hope this helps> >> > Tom> >> > --On 17 August 2007 19:02 +0200 Per Larsson <per.larsson at sbc.su.se> > > wrote:> >> >> Hello!> >>> >>> >> Check out> >> http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. > >> 2C_or_no_chan> >> ge_in_energy._Converged_to_machine_precision. > >> 2C_but_not_to_the_requested_> >> precision> >>> >>> >> Cheers> >> /Per> >>> >>> >>> >> 17 aug 2007 kl. 18.28 skrev Sheyore Omovie:> >>> >> Dear gmx-users,> >>> >> I have 2 molecules in a box, as usual pdb2gmx saw them as one. i > >> edited> >> the .top file to remove the bonds created between the two > >> molecules, I> >> also added a distance restraint btw the molecules. (The 2 > >> structures have> >> been separately minimized). However, I get the ff message for EM run:> >>> >> Stepsize too small, or no change in energy.> >> Converged to machine precision,> >> but not to the requested precision Fmax < 1000> >>> >> Double precision normally gives you higher accuracy.> >>> >> Steepest Descents converged to machine precision in 15 steps,> >> but did not reach the requested Fmax < 1000.> >> Potential Energy = 1.0246325e+20> >> Maximum force = inf on atom 1> >> Norm of force = inf I would appreciate any advice > >> on how> >> to fix this.> >> Rgds> >> John> >>> >>> >> __________________________________________________> >> See what you’re getting into?before you go there See it!> >> _______________________________________________> >> gmx-users mailing list gmx-users at gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/search before > >> posting!> >> Please don't post (un)subscribe requests to the list. Use the> >> www interface or send it to gmx-users-request at gromacs.org.> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php> >>> >>> >> >> >> > ----------------------> > TJ Piggot> > t.piggot at bristol.ac.uk> > University of Bristol, UK.> >> > _______________________________________________> > gmx-users mailing list gmx-users at gromacs.org> > http://www.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/search before > > posting!> > Please don't post (un)subscribe requests to the list. Use the> > www interface or send it to gmx-users-request at gromacs.org.> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> > _______________________________________________> Erik Marklund, PhD student> Laboratory of Molecular Biophysics,> Dept. of Cell and Molecular Biology, Uppsala University.> Husargatan 3, Box 596, 75124 Uppsala, Sweden> phone: +46 18 471 4537 fax: +46 18 511 755> erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys> > > _______________________________________________> gmx-users mailing list gmx-users at gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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